Last updated: 2022-02-10
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Knit directory: Serreze-T1D_Workflow/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | d199bd4 | Belinda Cornes | 2022-02-10 | QC analysis |
| Neogen_Sample_ID | Missing | AA | AC | AG | AT | CC | CG | GG | TC | TG | TT | GC | TA | Total_Genotyped | Percent_Genotyped | MURGIGV01_SNP.Count | cr |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| LQ01806 | 5944 | 33652 | 164 | 430 | 2 | 34382 | 1 | 34737 | 448 | 157 | 33342 | 0 | 0 | 137315 | 95.85% | 143259 | 0.958508714984748 |
| NG00186 | 5993 | 29201 | 1895 | 7713 | 5 | 29869 | 2 | 30221 | 7657 | 1790 | 28911 | 2 | 0 | 137266 | 95.82% | 143259 | 0.958166677137213 |
| LQ01807 | 5847 | 33705 | 143 | 395 | 2 | 34430 | 1 | 34796 | 413 | 152 | 33375 | 0 | 0 | 137412 | 95.92% | 143259 | 0.959185810315582 |
| NG00192 | 5925 | 28975 | 1943 | 8010 | 9 | 29647 | 4 | 30089 | 7947 | 1888 | 28814 | 5 | 3 | 137334 | 95.86% | 143259 | 0.958641341905221 |
| DF06129 | 5433 | 33931 | 138 | 329 | 0 | 34465 | 1 | 34773 | 349 | 119 | 33720 | 1 | 0 | 137826 | 96.21% | 143259 | 0.96207568110904 |
| NG00197 | 5396 | 29959 | 1640 | 6546 | 3 | 30770 | 5 | 31116 | 6587 | 1598 | 29632 | 4 | 3 | 137863 | 96.23% | 143259 | 0.96233395458575 |
| NG00485 | 5874 | 25573 | 3258 | 13556 | 13 | 26408 | 11 | 26672 | 13272 | 3148 | 25461 | 8 | 5 | 137385 | 95.90% | 143259 | 0.958997340481226 |
| NG00261 | 5926 | 28717 | 2067 | 8487 | 10 | 29472 | 8 | 29784 | 8306 | 1940 | 28535 | 4 | 3 | 137333 | 95.86% | 143259 | 0.958634361540985 |
| ML00983 | 6114 | 33592 | 172 | 549 | 3 | 34260 | 2 | 34588 | 566 | 177 | 33232 | 3 | 1 | 137145 | 95.73% | 143259 | 0.957322053064729 |
| NG00303 | 12067 | 29048 | 1674 | 6585 | 3 | 28279 | 2 | 28663 | 6445 | 1617 | 28871 | 3 | 2 | 131192 | 91.58% | 143259 | 0.915767944771358 |
| ML00984 | 7660 | 33451 | 226 | 702 | 3 | 33399 | 2 | 33754 | 720 | 244 | 33097 | 1 | 0 | 135599 | 94.65% | 143259 | 0.946530409956791 |
| NG00453 | 7688 | 29349 | 1810 | 7168 | 9 | 29411 | 7 | 29776 | 7098 | 1741 | 29197 | 4 | 1 | 135571 | 94.63% | 143259 | 0.9463349597582 |
| NG00158 | 5529 | 28525 | 2147 | 8837 | 8 | 29403 | 7 | 29715 | 8676 | 2013 | 28389 | 5 | 5 | 137730 | 96.14% | 143259 | 0.961405566142441 |
| NG00292 | 5575 | 30152 | 1562 | 6136 | 4 | 30944 | 6 | 31333 | 6109 | 1479 | 29953 | 4 | 2 | 137684 | 96.11% | 143259 | 0.961084469387613 |
| NG00160 | 5784 | 30366 | 1446 | 5692 | 7 | 31155 | 7 | 31567 | 5619 | 1352 | 30259 | 4 | 1 | 137475 | 95.96% | 143259 | 0.959625573262413 |
| NG00295 | 5488 | 28691 | 2135 | 8679 | 7 | 29460 | 7 | 29767 | 8555 | 2025 | 28434 | 6 | 5 | 137771 | 96.17% | 143259 | 0.961691761076093 |
| NG00161 | 5787 | 29971 | 1546 | 6414 | 8 | 30845 | 6 | 31108 | 6295 | 1522 | 29752 | 4 | 1 | 137472 | 95.96% | 143259 | 0.959604632169707 |
| NG00334 | 5524 | 30390 | 1394 | 5814 | 7 | 31311 | 4 | 31594 | 5707 | 1380 | 30130 | 1 | 3 | 137735 | 96.14% | 143259 | 0.961440467963618 |
| NG00165 | 10649 | 27497 | 2202 | 8861 | 10 | 27863 | 6 | 28096 | 8660 | 2141 | 27269 | 4 | 1 | 132610 | 92.57% | 143259 | 0.925666101257164 |
| NG00345 | 14528 | 27840 | 2154 | 8274 | 6 | 26189 | 5 | 26501 | 8159 | 2070 | 27524 | 6 | 3 | 128731 | 89.86% | 143259 | 0.898589268388024 |
| NG00203 | 5617 | 29453 | 1839 | 7331 | 5 | 30270 | 3 | 30535 | 7203 | 1776 | 29226 | 1 | 0 | 137642 | 96.08% | 143259 | 0.960791294089726 |
| NG00395 | 6053 | 29813 | 1621 | 6680 | 10 | 30580 | 7 | 30792 | 6502 | 1586 | 29608 | 4 | 3 | 137206 | 95.77% | 143259 | 0.957747855283089 |
| NG00183 | 7224 | 28973 | 1901 | 7882 | 7 | 29325 | 6 | 29607 | 7775 | 1793 | 28758 | 7 | 1 | 136035 | 94.96% | 143259 | 0.949573848763428 |
| NG00239 | 14913 | 29425 | 1618 | 6197 | 7 | 26828 | 2 | 27308 | 6233 | 1618 | 29103 | 4 | 3 | 128346 | 89.59% | 143259 | 0.895901828157393 |
| Neogen_Sample_ID | Provided.Sex | Inferred.Sex |
|---|---|---|
| LQ01806 | F | M |
| NG00186 | F | M |
| LQ01807 | F | M |
| NG00192 | F | M |
| DF06129 | F | M |
| NG00197 | F | M |
| NG00485 | F | M |
| NG00261 | F | M |
| ML00983 | F | M |
| NG00303 | F | M |
| ML00984 | F | F |
| NG00453 | F | F |
| NG00158 | F | M |
| NG00292 | F | M |
| NG00160 | F | M |
| NG00295 | F | M |
| NG00161 | F | M |
| NG00334 | F | M |
| NG00165 | F | M |
| NG00345 | F | M |
| NG00203 | F | M |
| NG00395 | F | M |
| NG00183 | F | F |
| NG00239 | F | F |
| Neogen_Sample_ID | age.of.onset | group | diabetic.status | strain |
|---|---|---|---|---|
| LQ01806 | 0.0 | (A2 Parental) | Diabetes Proj | NOD |
| NG00186 | 0.0 | EOI | ICI-No Diabetes | (F1 x NOD)BC1 |
| LQ01807 | 0.0 | (A2 Parental) | Diabetes Proj | NOD |
| NG00192 | 0.0 | EOI | ICI-No Diabetes | (F1 x NOD)BC1 |
| DF06129 | 0.0 | B6.g7 Parental | Both Projects | B6.NODIdd1 |
| NG00197 | 0.0 | EOI | ICI-No Diabetes | (F1 x NOD)BC1 |
| NG00485 | 0.0 | F1 | Diabetes Proj | (NODxB6.NODIdd1)F1 |
| NG00261 | 15.0 | ICI | T1D <17 | (F1 x NOD)BC1 |
| ML00983 | 0.0 | (DQ8 Parental) | Myocarditis | NOD |
| NG00303 | 12.3 | ICI | T1D <17 | (F1 x NOD)BC1 |
| ML00984 | 0.0 | (DQ8 Parental) | Myocarditis | NOD |
| NG00453 | 137.0 | ICI | T1D <17 | (F1 x NOD)BC1 |
| NG00158 | 0.0 | EOI | ICI-No Diabetes | (F1 x NOD)BC1 |
| NG00292 | 14.6 | ICI | T1D <17 | (F1 x NOD)BC1 |
| NG00160 | 0.0 | EOI | ICI-No Diabetes | (F1 x NOD)BC1 |
| NG00295 | 13.1 | ICI | T1D <17 | (F1 x NOD)BC1 |
| NG00161 | 0.0 | EOI | ICI-No Diabetes | (F1 x NOD)BC1 |
| NG00334 | 15.0 | ICI | T1D <17 | (F1 x NOD)BC1 |
| NG00165 | 0.0 | EOI | ICI-No Diabetes | (F1 x NOD)BC1 |
| NG00345 | 16.0 | ICI | T1D <17 | (F1 x NOD)BC1 |
| NG00203 | 0.0 | EOI | ICI-No Diabetes | (F1 x NOD)BC1 |
| NG00395 | 14.4 | ICI | T1D <17 | (F1 x NOD)BC1 |
| NG00183 | 0.0 | EOI | ICI-No Diabetes | (F1 x NOD)BC1 |
| NG00239 | 11.0 | ICI | T1D <17 | (F1 x NOD)BC1 |
| Neogen_Sample_ID | no_pheno | low_call.rate | different_sex |
|---|---|---|---|
| LQ01806 | XX | ||
| NG00186 | XX | ||
| LQ01807 | XX | ||
| NG00192 | XX | ||
| DF06129 | XX | ||
| NG00197 | XX | ||
| NG00485 | XX | ||
| NG00261 | XX | ||
| ML00983 | XX | ||
| NG00303 | XX | ||
| NG00158 | XX | ||
| NG00292 | XX | ||
| NG00160 | XX | ||
| NG00295 | XX | ||
| NG00161 | XX | ||
| NG00334 | XX | ||
| NG00165 | XX | ||
| NG00345 | XX | XX | |
| NG00203 | XX | ||
| NG00395 | XX | ||
| NG00239 | XX |
R version 3.6.2 (2019-12-12)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.7
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] tibble_3.1.2 readxl_1.3.1 cluster_2.1.0 dplyr_0.8.5
[5] optparse_1.6.6 rhdf5_2.28.1 mclust_5.4.6 tidyr_1.0.2
[9] data.table_1.14.0 knitr_1.33 kableExtra_1.1.0 workflowr_1.6.2
loaded via a namespace (and not attached):
[1] tidyselect_1.0.0 xfun_0.24 purrr_0.3.4 colorspace_2.0-2
[5] vctrs_0.3.8 htmltools_0.5.1.1 getopt_1.20.3 viridisLite_0.4.0
[9] yaml_2.2.1 utf8_1.2.1 rlang_0.4.11 later_1.0.0
[13] pillar_1.6.1 glue_1.4.2 lifecycle_1.0.0 stringr_1.4.0
[17] cellranger_1.1.0 munsell_0.5.0 rvest_0.3.5 evaluate_0.14
[21] httpuv_1.5.2 fansi_0.5.0 Rcpp_1.0.7 readr_1.3.1
[25] promises_1.1.0 scales_1.1.1 backports_1.2.1 webshot_0.5.2
[29] fs_1.4.1 hms_0.5.3 digest_0.6.27 stringi_1.7.2
[33] rprojroot_1.3-2 tools_3.6.2 magrittr_2.0.1 crayon_1.4.1
[37] whisker_0.4 pkgconfig_2.0.3 ellipsis_0.3.2 xml2_1.3.1
[41] assertthat_0.2.1 rmarkdown_2.1 httr_1.4.1 rstudioapi_0.13
[45] Rhdf5lib_1.6.3 R6_2.5.0 git2r_0.26.1 compiler_3.6.2